In this repository the R-Scrips and Rmarkdown reports of Prieto-Garcia et al. 2024 are provided.
R-Scripts and Rmarkdown reports have to be executed in the following order:
- 01_modulizer_output_to_rds.R
- 02_effect_of_USP39_KD_on_splicing.Rmd
- 03_get_read_support_for_A5SS_events.R
- 04_generate_peptide_and_adjusted_SWISSPROT_sequences.Rmd
- 05_adjust_IDs_for_FAS_analysis.R
- 06_FASscore_analysis.Rmd
These first rendered HTML-Reports can be accessed at https://mchicken1988.github.io/Prieto_Garcia_et_al_2023/
- 07_modulize_to_regulated_a5ss_rds.R
- 09_modulize_to_regulated_granges_rds.R
- 08_modulize_to_unregulated_granges_rds.R
- 10_figures_1_s4_garcia_et_al_2024.Rmd
the commands for the splicing analysis can be found in
- 11_majiq_porcession.Rmd